Same problem here: after upgrade to FC4, mysqld cannot start since its
permission tables wrere in the ISAM format.
A solution if you have already upgraded to FC4:
To convert the tables you need to temporarily downgrade MySQL to a version with
ISAM support. To do so, stop mysqld and all processes accessing it, then
download and install the RPM files from Fedora Core 3:
# rpm --nodeps --oldpackage -Uvh \
mysql-3.23.58-16.FC3.1.i386.rpm \
mysql-server-3.23.58-16.FC3.1.i386.rpm \
perl-DBD-MySQL-2.9003-5.i386.rpm
You may need to add "--nodeps" to override dependency problems (e.g., from
php-mysql).
Now, as advised above, run:
$ /usr/bin/mysql_convert_table_format mysql --user='foo' --password='bar'
Repeat this, replacing the "mysql" argument with each of the ISAM databases you
have (look at /var/lib/mysql).
Finally, reinstall the Fedora Core 4 packages:
# yum install mysql mysql-server perl-DBD-MySQL
As you can see this procedure is rather violent, so it's a good idea to back up
your data first.

Apparently the MySQL folk decided that ISAM shouldn't be built by default anymore as of 4.x. I've re-
enabled it in our latest build (4.1.12-1 and up). It's probably still a good idea to reconstruct any old
tables you have, as it's not hard to read the handwriting on the wall ... but we'll hold the line for a little
while yet.